Is there any chance that you've replaced the fonts, either on the Reader itself, or in the eBook Library Windows software app's folders, as this sounds like what happens when there's a mismatch between the two fonts, as the Sony software tries to calculate the page sizes using the font size.
You could try using Calibre to copy files to the device & see if that has any effect (AIUI, you'll need to install the PRS-500 USB driver) as that will transfer the book but the device will have to do the formatting (pagination) itself when first read.
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